Part I is below,
Part II is here.
TA:
Olga Zhaxybayeva
Meeting times and places:
Usually Mondays 2-4 p.m. TLS301, Wednesdays 1-4 p.m. M037
Exceptions: Feb. 4 (M037) and Feb. 6 (Kresge library, TLS 2nd floor).
See here for details
!!! Exam 1 is posted here !!!
Return by Thursday, March 28, 5 pm, in person.
Sample answers are here.
Tentative list of topics for student presentations
Links to notes and assignments of individual classes:
Class 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13
Class 13: Student Project and PUZZLE continued
Class 12: Among site rate variation, models for nucleaotide substitution, discussion of ml-ratio tests
Class 11: TREE-PUZZLE exercises: ml-mapping, ml-ratio test, among site rate variation
Class 10: PUZZLE, ml-mapping, ml-ratio tests
Class 9: PHYLIP: distance, parsimony, and maximum likelihood analyses using DNA and Protein sequences
Class 8: Neutral evolution and genetic drift, "cladistics", Phylip, and LBA
Class 7: Assignments #4, alignment and trees with clustalx
Class 6: Trees, homology revisited, gene and genome duplications.
Class 5: Sequence alignment - Principle and practice, tree with clustal, treeview
Class 4: Genome analyses, the search for distant homologues, and detection of atypical patterns of relationship (in M037)
Class 3: PRSS, Blast2Seq, BLAST and PSI BLAST (in M037)
Class 2: Why should you care? Overview and BLAST/PSI-BLAST (in TLS 301)
Class 1: Introduction, Entrez, Blink, Databanks at NCBI (in M037)
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Molecular Evolution : A Phylogenetic Approach by Roderic D. M. Page, Edward C. Holmes Buy@Amazon.com This book gives an excellent introduction to terms, methods, and problems in molecular evolution. It does not contain too many details on individual algorithm, but it provides a very readable overview. |
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Molecular Evolution by Wen-Hsiung Li Buy@Amazon.com Well written, gives good background, especially with respects to the biological aspects of evolution. |
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Fundamentals of Molecular Evolution, Second Edition
by Dan Graur and Wen-Hsiung Li More details and formulas on algorithms, but fewer examples. |
| Bioinformatics : A Practical Guide to the Analysis of
Genes and Proteins (2nd Edition) by Andreas D. Baxevanis, B. F. Francis Ouellette Buy@Amazon.com The book gives an overview of many available computational tools. It focuses on the practical aspects of how to use the programs rather then on how the methods work from theoretical point of view. Good to use as a reference book. |
| |
Phylogenetics Trees Made Easy : A How-To Manual for Molecular
Biologists by Barry G. Hall A cookbook of methods and programs for phylogenetic analyses. More info at the book's Home Page. In contrast to the impression generated by the book, MrBayes is useful for protein sequences. |
| Molecular Systematics by David M. Hillis (Editor), Craig Moritz (Editor), Barbara K. Mable (Editor) Buy@Amazon.com Chapter 11. Phylogenetic Inference. A lot of data and information on how to make trees. It does not make for an easy reading experience. Only recommended to look things up in more detail. |
